Mitochondria analytics

Visualization and analysis tools for analyzing mitochondria in the Layer 2/3 EM volume

visualize all mitochondria in a cell of interest


Contents

Visualization tools

Visualize a single mitochondrion of interest in Neuroglancer

neuroglancer_link_generator_mitochondria_visualization_version.ipynb: generate a Neuroglancer link for a single cellid and single mitochondrion from the pni_mito_cellswskel_v185_fullstats.csv datatable. The view will be centered at the centroid of the mitochondrion in the volume.

neuroglancer link to a single mitochondrion with crosshair at the mito centroid


Visualize all mitochondria in a neuron of interest in Neuroglancer

neuroglancer_link_generator_all_mitochondria.ipynb: generate a Neuroglancer link for all the mitochondria in a single cellid of interest pulling the mito ids from the 211019_mitochondria_info.csv datatable.

neuroglancer link generator for all mitochondria in a cell

Visualize neuronal mitochondria by compartment in Neuroglancer

neuroglancer_link_generator_neuronalmitochondria_bycompartment.ipynb: as above, but allows to select for a compartment of interest. Neuronal compartment assignments are based on the method described by Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity Turner et al, Cell 2022.

neuroglancer link generator for mitochondria by compartment

3D visualizer of all mitochondria in a cell of interesting using Meshparty, vtk, and OpenGL viewer

vtk_mitochondria_visualizer.ipynb: generate a 3D interactive view of all mitochondria in a cell of interest. Note this method has significant file download and space requirements compared to using the Neuroglancer viewer.

3D visualizer of all mitochondria in a cell

3D visualizer of all mitochondria and synapses in a cell of interesting using Meshparty, vtk, and OpenGL viewer

vtk_mitochondria_visualizer_with_synapses.ipynb: generate a 3D interactive view of all mitochondria in a cell of interest along with the pre- and post-syanptic sites. Note this method has significant file download and space requirements compared to using the Neuroglancer viewer.

3D visualizer of all mitochondria and synapses in a cell

3D vector plots by cellid lookup by neuronal subtype

mitochondria_3d_vector_plots_by_cellid_lookup_by_neuronal_subtype.ipynb: generate 3D interactive scatterplots in Plotly, 3D quiver plots in matplotlib, and a Neuroglancer views with this notebook. Uses a dataframe that generates spatial and vector calculations from the original mitochondria dataframe by Turner et al. Download mito_above_soma.csv in the data folder.

3D quiver plot of mito centroid with bounding box distance vector

3D visualization for mitochondria within a 45 degree cone above soma

3dvisualizer_for_withincone.ipynb: generate 3D interactive scatterplots in Plotly, 3D quiver plots in matplotlib, and Neuroglancer views with this notebook. Uses a dataframe that generates spatial, vector, and cone angle calculations from the original mitochondria dataframe by Turner et al. Download pyr_all.csv in the data folder. Special thanks to Qiao Liu and Wanwen Zeng at Stanford for their assistance in debugging the code.

3D scatterplot using Plotly for visualizing mitochondria within a 45 degree cone above soma